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Xinglab / TideHunter

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
https://github.com/yangao07/TideHunter
MIT License
18 stars 2 forks source link

Core dump when using HPC-kmer #17

Open palakpsheth opened 1 year ago

palakpsheth commented 1 year ago

hey there getting a core dump only when using the -H option. Full cmd:

~/TideHunter-v1.5.4/bin/TideHunter -H --kmer-length 8 --window-size 5 --min-copy 3 --min-period 41 --min-len 41 --out-fmt 2 --thread 19 unmapped.trimmed.fastq.gz > unmapped.trimmed.tidehunter.tsv
double free or corruption (out)
Aborted (core dumped)

Thank you!

yangao07 commented 1 year ago

Hi, the HPC-kmer mode does not give us much improvement in our data, so it is not never carefully evaluated.

Can you share the data that lead to the fault?

palakpsheth commented 1 year ago

thank you for your reply @yangao07. I cant upload more than 25mb here but this is an example file of the datatypes unmapped.trimmed.fastq.gz

finding the tool very useful thank you!

yangao07 commented 1 year ago

Hi, sorry for the late reply. Just fixed a bug that is due to very short input sequence. It should work now!

palakpsheth commented 1 year ago

@yangao07 thank you for the fix! i can confirm that it no longer core-dumps for my samples